As an option fine, but I would avoid including by default in boolean commands for three reasons:
MergeAllFaces can take a long while to run, and I would rather not wait for it in cases where I don’t need it.
MergeAllFaces not infrequently returns an invalid object. At present I can undo it without affecting the prior boolean and then decide if I want to manually extract faces and cap.
Boolean operations already fail all too often. I suspect this would cause more failures and make them more difficult to diagnose.